[Bioperl-l] Re: Installing BioPerl under Mac OS X

Thu Oct 21 06:21:13 EDT 2004

I had a similar experience.  Also, with a continuously evolving project  
like bioperl, I have found it advantageous to have the CVS versions  
available.

Sean

On Oct 21, 2004, at 1:27 AM, Madeleine Lemieux wrote:

> Koen,
>
>>> I have also installed (following each package's installation  
>>> instructions) wwwBlast (latest OS X version from NCBI), t-coffee  
>>> (the Unix version, not the Mac one), clustalw (the OS X version) and  
>>> EMBOSS.
>>
>> Just as a note, all three, as well as pTk (804.026) are also availble  
>> through fink.
> My fink (0.7.1) does not list clustalw, pTk, t-coffee or wwwBlast  
> among its packages so I just downloaded the source or executables that  
> were available. I've used fink several times but don't know much about  
> it. Is there some way other than using the list option to find out  
> what packages are available?
>
>> Madeleine, I am curious why didn't use fink to install bioperl.  
>> Version 1.4 has been available for a few months, and is actually part  
>> of the most recent binary release (Fink 0.7.1). Did you get any  
>> particular errors when you tried to install it? I am the  
>> fink-maintainer of bioperl, so if there are any problems please let  
>> me know, so I can try to fix the package.
> I was quite pleased to see bioperl as one of the fink packages but see  
> below for what happens when I try use fink to install bioperl-pm581.  
> Is there a log file somewhere that might contain more useful  
> information?
>
> Madeleine
>
> -----------
> LeMeiLin:~ $ fink install bioperl-pm581
> /usr/bin/sudo /sw/bin/fink  install bioperl-pm581
> Password:
> Information about 1853 packages read in 1 seconds.
> The following package will be installed or updated:
>  bioperl-pm581
> The following 10 additional packages will be installed:
>  libwww-pm581 libxml-pm581 soap-lite-pm581 uri-pm581 xml-dom-pm581
>  xml-node-pm581 xml-parser-pm581 xml-regexp-pm xml-twig-pm581  
> xml-writer-pm
> Do you want to continue? [Y/n] Y
> gzip -dc /sw/src/URI-1.30.tar.gz | /sw/bin/tar -xf -  --no-same-owner  
> --no-same-permissions
> /usr/bin/perl5.8.1 Makefile.PL PERL=/usr/bin/perl5.8.1 PREFIX=/sw  
> INSTALLPRIVLIB=/sw/lib/perl5/5.8.1  
> INSTALLARCHLIB=/sw/lib/perl5/5.8.1/darwin-thread-multi-2level  
> INSTALLSITELIB=/sw/lib/perl5/5.8.1  
> INSTALLSITEARCH=/sw/lib/perl5/5.8.1/darwin-thread-multi-2level  
> INSTALLMAN1DIR=/sw/share/man/man1 INSTALLMAN3DIR=/sw/share/man/man3  
> INSTALLSITEMAN1DIR=/sw/share/man/man1  
> INSTALLSITEMAN3DIR=/sw/share/man/man3 INSTALLBIN=/sw/bin  
> INSTALLSITEBIN=/sw/bin INSTALLSCRIPT=/sw/bin
> Checking if your kit is complete...
> Looks good
> Writing Makefile for URI
> make
> cp URI/nntp.pm blib/lib/URI/nntp.pm
> cp URI/gopher.pm blib/lib/URI/gopher.pm
> cp URI/rlogin.pm blib/lib/URI/rlogin.pm
> cp URI/https.pm blib/lib/URI/https.pm
> cp URI/snews.pm blib/lib/URI/snews.pm
> cp URI/URL.pm blib/lib/URI/URL.pm
> cp URI/Split.pm blib/lib/URI/Split.pm
> cp URI/_userpass.pm blib/lib/URI/_userpass.pm
> cp URI/urn/isbn.pm blib/lib/URI/urn/isbn.pm
> cp URI/mailto.pm blib/lib/URI/mailto.pm
> cp URI/file/QNX.pm blib/lib/URI/file/QNX.pm
> cp URI/_login.pm blib/lib/URI/_login.pm
> cp URI/ldapi.pm blib/lib/URI/ldapi.pm
> cp URI/file/Unix.pm blib/lib/URI/file/Unix.pm
> cp URI/_segment.pm blib/lib/URI/_segment.pm
> cp URI/_query.pm blib/lib/URI/_query.pm
> cp URI/mms.pm blib/lib/URI/mms.pm
> cp URI/file/Mac.pm blib/lib/URI/file/Mac.pm
> cp URI/urn.pm blib/lib/URI/urn.pm
> cp URI/_ldap.pm blib/lib/URI/_ldap.pm
> cp URI/Heuristic.pm blib/lib/URI/Heuristic.pm
> cp URI/rsync.pm blib/lib/URI/rsync.pm
> cp URI/ssh.pm blib/lib/URI/ssh.pm
> cp URI/WithBase.pm blib/lib/URI/WithBase.pm
> cp URI/pop.pm blib/lib/URI/pop.pm
> cp URI/file/Base.pm blib/lib/URI/file/Base.pm
> cp URI/file/Win32.pm blib/lib/URI/file/Win32.pm
> cp URI/_foreign.pm blib/lib/URI/_foreign.pm
> cp URI.pm blib/lib/URI.pm
> cp URI/file/FAT.pm blib/lib/URI/file/FAT.pm
> cp URI/news.pm blib/lib/URI/news.pm
> cp URI/ldap.pm blib/lib/URI/ldap.pm
> cp URI/_generic.pm blib/lib/URI/_generic.pm
> cp URI/rtsp.pm blib/lib/URI/rtsp.pm
> cp URI/ftp.pm blib/lib/URI/ftp.pm
> cp URI/Escape.pm blib/lib/URI/Escape.pm
> cp URI/_server.pm blib/lib/URI/_server.pm
> cp URI/http.pm blib/lib/URI/http.pm
> cp URI/ldaps.pm blib/lib/URI/ldaps.pm
> cp URI/file.pm blib/lib/URI/file.pm
> cp URI/QueryParam.pm blib/lib/URI/QueryParam.pm
> cp URI/file/OS2.pm blib/lib/URI/file/OS2.pm
> cp URI/sip.pm blib/lib/URI/sip.pm
> cp URI/urn/oid.pm blib/lib/URI/urn/oid.pm
> cp URI/telnet.pm blib/lib/URI/telnet.pm
> cp URI/tn3270.pm blib/lib/URI/tn3270.pm
> cp URI/rtspu.pm blib/lib/URI/rtspu.pm
> cp URI/sips.pm blib/lib/URI/sips.pm
> cp URI/data.pm blib/lib/URI/data.pm
> Manifying blib/man3/URI::Escape.3pm
> Manifying blib/man3/URI.3pm
> Manifying blib/man3/URI::URL.3pm
> Manifying blib/man3/URI::ldap.3pm
> Manifying blib/man3/URI::file.3pm
> Manifying blib/man3/URI::data.3pm
> Manifying blib/man3/URI::WithBase.3pm
> Manifying blib/man3/URI::QueryParam.3pm
> Manifying blib/man3/URI::Heuristic.3pm
> Manifying blib/man3/URI::Split.3pm
> make test
> PERL_DL_NONLAZY=1 /usr/bin/perl5.8.1 "-MExtUtils::Command::MM" "-e"  
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/abs............ok
> t/clone..........ok
> t/data...........ok
> t/escape.........ok
> t/file...........ok
> t/ftp............ok
> t/generic........ok
> t/heuristic......FAILED test 7
>         Failed 1/15 tests, 93.33% okay
> t/http...........ok
> t/ldap...........ok
> t/mailto.........ok
> t/mix............ok
> t/mms............ok
> t/news...........ok
> t/old-absconf....ok
> t/old-base.......ok
> t/old-relbase....ok
> t/pop............ok
> t/query-param....ok
> t/query..........ok
> t/rel............ok
> t/rfc2732........ok
> t/roy-test.......ok
> t/rsync..........ok
> t/rtsp...........ok
> t/sip............ok
> t/split..........ok
> t/storable.......ok
> t/urn-isbn.......skipped
>         all skipped: Needs the Business::ISBN module installed
> t/urn-oid........ok
> Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/heuristic.t               15    1   6.67%  7
> 1 test skipped.
> Failed 1/30 test scripts, 96.67% okay. 1/447 subtests failed, 99.78%  
> okay.
> make: *** [test_dynamic] Error 2
> ### execution of make failed, exit code 2
> Failed: compiling uri-pm581-1.30-11 failed
> LeMeiLin:~ $
>
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